FMO DATABASE

FMODB ID: KGV43

Calculation Name: 3EPU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EPU

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZNP3

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1248200.869537
FMO2-HF: Nuclear repulsion	1191925.925615
FMO2-HF: Total energy	-56274.943922
FMO2-MP2: Total energy	-56436.282896

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-1.61	0.265	-0.022	-0.831	-1.022	0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.013

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	SER	0	0.010	-0.023	3.816	0.469	2.201	-0.021	-0.813	-0.898	0.002
4	A	4	ARG	1	0.923	0.950	6.383	0.534	0.534	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.083	0.053	8.747	0.143	0.143	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.766	-0.866	7.541	-0.869	-0.869	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.877	0.932	4.629	-1.515	-1.372	-0.001	-0.018	-0.124	0.000
8	A	8	LEU	0	0.020	0.025	8.524	0.091	0.091	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.020	0.020	11.967	0.030	0.030	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.919	0.967	8.586	-0.622	-0.622	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.060	-0.036	11.230	0.024	0.024	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.031	0.015	13.386	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.026	-0.041	13.968	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.002	-0.013	11.937	0.013	0.013	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.869	0.965	15.893	-0.315	-0.315	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.005	-0.003	18.625	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.069	-0.025	19.136	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.008	0.012	17.942	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.866	-0.908	14.206	0.489	0.489	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.081	-0.055	14.719	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.002	0.007	16.262	-0.045	-0.045	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.006	-0.011	11.475	0.028	0.028	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.065	-0.029	12.331	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.780	-0.887	13.764	-0.212	-0.212	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.961	-0.990	15.510	-0.271	-0.271	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.029	0.001	16.552	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.759	0.862	11.434	0.550	0.550	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.005	-0.001	16.858	0.027	0.027	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.012	0.009	16.839	0.013	0.013	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.002	0.009	19.035	0.010	0.010	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.013	-0.007	19.995	0.016	0.016	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.010	-0.007	23.579	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.004	0.020	24.099	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.866	-0.943	27.537	0.074	0.074	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.097	-0.054	29.896	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.932	0.977	31.376	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.041	0.010	29.442	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.957	0.983	28.055	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.031	0.033	23.139	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.011	-0.002	22.547	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.001	0.002	17.913	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.008	-0.004	19.092	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.006	0.007	14.310	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.035	0.007	15.353	-0.064	-0.064	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.023	0.022	16.573	-0.070	-0.070	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.011	-0.004	10.990	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.936	-0.974	12.785	-0.260	-0.260	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.031	-0.019	15.527	0.040	0.040	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.024	-0.005	14.866	-0.040	-0.040	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.046	0.009	18.184	0.021	0.021	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.020	0.008	21.594	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.004	-0.013	23.750	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.066	0.023	26.567	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.044	-0.045	27.152	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.056	-0.016	31.243	0.007	0.007	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.086	0.055	34.765	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.918	0.951	36.455	0.015	0.015	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.043	-0.018	39.226	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.005	0.002	42.307	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.918	-0.961	45.816	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.087	-0.031	47.812	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	ASN	0	0.108	0.067	49.420	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.070	-0.065	49.854	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.053	0.037	45.588	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.021	0.002	43.718	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.021	-0.007	43.639	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.919	-0.947	45.653	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.014	0.005	40.568	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.016	-0.015	40.134	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.017	-0.003	42.039	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.010	0.003	41.072	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	ASN	0	0.053	0.012	36.169	0.004	0.004	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.027	-0.003	38.690	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	74	TRP	0	0.006	0.017	37.882	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.034	0.022	35.226	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.009	0.017	35.740	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.997	-0.997	36.740	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.085	-0.048	37.217	0.005	0.005	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.060	-0.026	32.304	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.014	-0.006	31.828	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.044	-0.036	29.732	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.008	0.007	30.685	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.023	-0.006	32.490	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	CYS	0	-0.077	-0.046	32.341	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.008	0.000	34.717	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.822	-0.918	31.514	-0.074	-0.074	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.005	-0.021	34.113	0.008	0.008	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.069	-0.027	30.981	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.044	0.021	32.029	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.017	-0.020	34.079	0.009	0.009	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.008	-0.022	33.752	0.006	0.006	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.010	0.001	35.336	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.027	-0.021	29.458	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.005	0.019	31.532	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.009	-0.006	27.819	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.036	0.013	25.477	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.041	-0.025	21.901	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.032	0.022	16.884	0.015	0.015	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.058	0.024	18.844	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.016	-0.028	12.285	0.030	0.030	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.065	-0.020	14.655	0.039	0.039	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.920	-0.965	15.991	0.024	0.024	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.061	-0.022	14.505	0.024	0.024	0.000	0.000	0.000	0.000
104	A	104	SER	0	0.012	-0.009	15.271	0.037	0.037	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.038	0.005	15.521	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.903	-0.958	17.160	0.270	0.270	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.959	0.980	19.943	-0.130	-0.130	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.012	0.017	16.924	-0.020	-0.020	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.872	-0.952	20.451	0.180	0.180	0.000	0.000	0.000	0.000
110	A	110	CYS	0	-0.043	-0.009	22.721	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.876	-0.945	23.006	0.022	0.022	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.020	-0.022	20.845	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.868	-0.932	25.101	0.072	0.072	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.013	-0.002	28.142	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.014	-0.001	26.962	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.035	0.013	27.192	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.897	0.939	30.829	-0.062	-0.062	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.023	-0.013	32.667	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.053	-0.020	31.038	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.963	-0.979	34.644	0.035	0.035	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.016	-0.007	36.963	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.010	0.013	36.985	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.053	-0.041	34.797	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.040	-0.019	40.533	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.013	0.024	41.618	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.053	-0.037	41.245	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.026	-0.001	43.867	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.905	-0.956	46.164	0.012	0.012	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.913	0.953	47.070	0.002	0.002	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.044	-0.004	49.272	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.054	-0.027	46.914	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	132	THR	0	0.017	-0.002	43.475	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.021	0.000	38.460	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.894	-0.947	38.946	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.006	-0.012	36.799	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.995	-0.988	34.533	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)